Enzymologia pojedynczych cząsteczek RNA : wykorzystanie techniki FRET w badaniach zwijania się i dynamiki konformacyjnej rybozymów

• Autorzy: Hajdziona M. , Molski A.

Warianty tytułu

EN

Single-molecule RNA enzymology : using FRET to explore folding and conformational dynamics of ribozymes

• Języki publikacji: PL

Abstrakty

EN

Ribozymes are biologically important macromolecules that play a crucial role in cell metabolism and functions. Knowledge of folding and catalytic properties of ribozymes can be useful in biotechnology and medicine. In this work, we present a review of single-molecule RNA enzymology with particular emphasis on folding and catalysis observed with single-molecule FRET. Single-molecule spectroscopy provides insight into behaviors of individual molecules without averaging inherent in bulk measurements. In the first section we introduce ribozymes as RNA enzymes [1, 2]. In the second section, we present the structure of RNA molecules and examples of reaction mechanisms (Fig. 1) and function of different types of ribozymes (Fig. 2–5). Next, we review single-molecule FRET spectroscopy (Fig. 6, 7, Eqs. 1, 2). In the fourth section, we present examples of folding dynamics of ribozymes. In the fifth part, we focus on ribozyme catalysis (Fig. 8, 9). We discuss the coupling of conformational dynamics with catalytic reactions. In the last part we present methods of data analysis that can be used to obtain the kinetic rates from single molecule FRET experiments (Fig. 10).

Słowa kluczowe

PL

rybozymy; spektroskopia fluorescencyjna pojedynczych cząsteczek; FRET

EN

ribozymes; single-molecule fluorescence spectroscopy; FRET

• Wydawca: Polskie Towarzystwo Chemiczne
• Czasopismo: Wiadomości Chemiczne
• Rocznik: 2010
• Tom: [Z] 64, 3-4
• Strony: 173--193
• Opis fizyczny: bibliogr. 45 poz., schem., wykr.

Twórcy

autor

Hajdziona M.

autor

Molski A.

• Pracownia Dynamiki Procesów Fizykochemicznych, Wydział Chemii, Uniwersytet im. Adama Mickiewicza ul. Grunwaldzka 6, 60-780 Poznań,

Bibliografia

• [1] T.R. Cech, Biosci. Rep. 1990, 10, 317.
• [2] S. Altman, Biosci. Rep. 1990, 10, 239.
• [3] N.G. Walter, D.R. Engelke, Biologist, 2002, 49, 199.
• [4] X. Zhuang, Ann. Rev. Biophys. Struct., 2005, 34, 399.
• [5] S. Myong, B.C. Stevens, T. Ha, Structure, 2007, 14, 633.
• [6] M.A. Ditzler, E.A. Aleman, D. Rueda, N.G. Walter, Biopolymers, 2007, 87, 302.
• [7] R. Zhao, D. Rueda, Methods, 2009, 49, 112.
• [8] K.S. Karunatilaka, D. Rueda, Chem. Phys. Lett. 2009, 476, 1.
• [9] X. Chen, A.D. Ellington, Chem.Biodiversity, 2007, 4, 633.
• [10] N.G. Walter, S.A. Woodson, R.T. Batey, Non-Protein Coding RNAs, Springer Series in Biophysics, 2008.
• [11] J.J. Agresti, B.T. Kelly, A. Jaschke, A.D. Griffiths, PNAS, 2005, 102, 16170.
• [12] H.D. Kim, G.U. Nienhaus, T. Ha, J.W. Orr, J.R. Williamson, S.Chu, PNAS, 2002, 99, 4284.
• [13] V. Gopalan, PNAS, 2007, 104, 2031.
• [14] Y. Kobitski, A. Nierth, M. Helm, A. Jaschke, G.U. Nienhaus, Nucl. Ac. Research, 2007, 35, 2047.
• [15] R. Wombacher, S. Keiper, S. Suhm, A. Serbanov, D.J. Patel, A. Jaschke, Angew. Chem. Int. Ed, 2006, 45, 2469.
• [16] M.K. Nahas, T.J. Wilson, S. Hohng, K. Jarvie, D.M.J. Lilley, T. Ha Nature Struct. Mol. Biol., 2004, 11, 1107.
• [17] E. Tan, T.J. Wilson, M.K. Nahas, R.M. Clegg, D.M.J. Lilley, T. Ha, PNAS, 2003, 100, 9308.
• [18] T.J. Wilson, M. Nahas, T. Ha, D.M.J. Lilley, Biochem. Soc. Trans., 2005, 33, 461.
• [19] S. Liu, G. Bokinsky, N.G. Walter, X. Zhuang, PNAS, 2007, 104, 12639.
• [20] G. Bokinsky, D. Rueda, V.K. Misra, M.M. Rhodes, A. Gordus, H.P. Babcock, N.G. Walter, X. Zhuang, PNAS, 2003, 100, 9302.
• [21] X. Zhuang, H. Kim, M.J.B. Pereira, H.P. Babcock, N.G. Walter, S. Chu, Science, 2002, 296, 1473.
• [22] D. Rueda, G. Bokinsky, M.M. Rhodes, M.J. Rust, X. Zhuang, N.G. Walter, PNAS, 2004, 101, 10066.
• [23] N.G. Walter, K.J. Hampel, K.M. Brown, J.M. Burke, EMBO, 1998, 17, 2378.
• [24] N.G. Walter, J.M. Burke, D.P. Millar, Nat. Str. Biol., 1999, 6, 544.
• [25] E. Kikovska, S.G. Svard, L.A. Kirsebom, PNAS, 2007, 104, 2062.
• [26] M. Dahan, A.A. Deniz, T. Ha, D.S. Chemla, P.G Schultz, S. Weiss, Chem. Phys., 1999, 245, 85.
• [27] Z. Xie, N. Srividya, T. R. Sosnick, T. Pan, N. F. Scherer, PNAS, 2004, 101, 534.
• [28] S. Weiss, Science, 1999, 283, 1676.
• [29] R. Roy, S. Hohng, T. Ha, Nature Meth., 2008, 6, 507.
• [30] D. Herschlag, T.R. Cech, Biochemistry, 1990, 29, 10159.
• [31] R. Russell, D. Herschlag, J. Mol. Biol., 2001, 308, 839.
• [32] R. Russel, X. Zhuang, H.P. Babcock, I.S. Millett, S. Doniach, S. Chu, D. Herschlag, PNAS, 2002, 99, 155.
• [33] X. Zhuang, L. E. Bartley, H P. Babcock, R. Russel, T. Ha, D. Herschlag, S. R. Chu, Science, 2000, 288, 2048.
• [34] T. H. Lee, L.J. Lapidus, W. Zhao, K.J. Travers, D. Herschlag, S. Chu, Biophys. J., 2007, 92, 3275.
• [35] Z. Xie, N. Srividya, T.R. Sosnick, T. Pan, N.F. Scherer, PNAS, 2004, 101, 534.
• [36] X. Fang, T. Pan, T.R. Sosnick, Nature Str. Biol., 1999, 6, 1091.
• [37] P. Toti, L. Sbordone, C. Sbordone, C. Bauer, J. Biol. Phys., 2006, 32, 473.
• [38] T. Persson, S. Cuzic, R.K. Hartmann, J. Biol. Chem., 2003, 278, 43394.
• [39] E. Barkai , F. Brown, M. Orrit, H. Yang (Eds.), Theory and Evaluation of Single Molecule Signals, World Scientific, 2008.
• [40] M. Lippitz, F. Kulzer, M. Orrit, ChemPhysChem, 2005, 6, 770.
• [41] S.A. McKinney, Ch. Joo, T. Ha, Biophys. J., 2006, 91, 1941.
• [42] I. Gopich, A. Szabo, J. Phys. Chem. B, 2009, 113, 10965.
• [43] G. Haran, Chem. Phys., 2004, 307, 137.
• [44] L.R. Rabiner, Proc. IEEE, 1989, 77, 257.
• [45] T.H. Lee, J. Phys. Chem. B, 2009, 113, 11535.